Prepared
by Terror666
Summary: What if someone had believed her and Commander Shepard was given the chance to help prepare for the Reapers arrival


**Disclaimer: **I don't own anything in this story.

**Prepared**

Commander Jane Shepard stood before her office window looking out over the cityscape of Vancouver, the home of Alliance High Command. The report in her hand mostly forgotten as she watched the child playing on the neighboring rooftop. As she watched that display of innocence she hoped that what she was doing and had been doing would be enough to preserve that innocence.

The door behind her opened and lieutenant James Vega walked in without so much as a by your leave. She turned to the scarred and heavily muscled man who saluted. "Commander" "You don't have to salute me anymore James." She chided in a friendly tone. They had been working together for some time now as they were two of the three people in the alliance who had any experience with Reaper forces and in that time had become good friends, after some initial trouble caused by Shepard's time with Cerberus and James' mission on Fehl Prime. "Yeah, you said but the marines taught me proper military etiquette." trying to out do the Commander and failing. "Really? In my day they taught us useful things like fighting." Whatever might be said about her she definitely had a sharp wit. Usual banter over with Vega sober and said "We gotta go. The defense comity wants to see you." Shepard stiffened at this the comity did not call on someone unless it was important and then they made an appointment, to be called to them immediately meant trouble. "Must be important." She replied before tossing down the report in her hand and following the lieutenant out.

"What's going on?" She asked hoping the comity had told him something, just so she knew what she was walking into. Goddess. I hope its not more diplomatic cloak and dagger crap, this fake jail time is bad enough. She thought but did not voice.

After Shepard had been forced to destroy the Bahak system to delay the Reaper invasion she had turned herself and her ship, which was oh so lovingly built by Cerberus for her, over to the Alliance and was taken into custody. Or at least that is what they told everyone, what really happened was that she had a rather large portion of the Alliance top brass who believed her. Most important of them Admiral Hackett who had been promoted to Chief of Naval Operations in the wake of the Alliance victory over Sovereign and Captain then Councilor then Admiral Anderson. With them and several others in her corner she was able to not only avoid charges over the Bahak system but also be put in charge of the Anti Reaper Task Force. But to the outside galaxy especially the Council who did not believe her and the Batarians who were out for her blood it had to look like she was being punished, they simply could not afford a war on the eve of the Reaper invasion.

"Couldn't say. Just told me they needed you." She nodded at this. Figures they never tell you what you need even though all they do is talk. After that vicious thought passed trough her mind she spotted her CO admiral Anderson striding purposefully towards them. "Anderson" Shepard greeted. "Admiral" the lieutenant said saluting Anderson.

"You look good Shepard." the Admiral said while shaking Shepard's hand before patting her stomach and joking "Maybe a little soft around the edges. How are you holding up after being relieved of command?" Jane almost growled at her friend how dare he imply she was soft the only time in her life she had been in better shape was just after she had healed up from graduating N School. But since growling at ones superior was not considered wise she instead said "It's not so bad sir. Once you get used to the hot food and soft beds." Anderson was of course completely oblivious to her inner rage at him and continued with "We'll get it sorted out." During this exchange they were constantly dodging personnel hurrying about there business as the trio moved to there destination. Shepard was beginning to get really worried this level of activity was not normal couple that with being called before the defense comity spelled trouble for the Alliance possibly Reaper trouble or equally troubling a Batarian punitive invasion of Alliance space.

Needing to know what was happening Jane asked "What's going on, why is everyone in such a hurry?" "Admiral Hackett is mobilizing the fleets." this made Shepard stop "I am guessing word's made it to Alliance Command. Something big is headed our way." "The Reapers?" Asked the commander not really knowing which answer she wanted the Reapers were the stuff of nightmares but at least that would not be her fault like a Batarian invasion. "We don't know not for certain." That meant it was not the Batarians they would know that. Jane felt a rather strange sense of relief when she realized it was not her fault. "What else could it be?" She said that she knew it could not be the Batarians. "If I knew that" Anderson said without finishing. Shepard who was intimately familiar with Alliance defenses and how they would most likely stack up said "You know we're not ready if it is them, not yet anyway."

The plans she and her task force had come up with would not be fully complete for another six months for the inner systems and another two years for the outer colonies. Some things were in place but not all she wanted or planned.

"Tell that to the defense comity" Anderson said while moving up a set of stairs continuing there trip up to said comity.

"Unless we're planning to talk the Reapers to death, the comity is a waist of time." The defense comity was actually very useful in peace time, because they were the ones who planned and developed strategies for when war did break out but once that happened they lost a lot of there use, because it would be officers like Hackett, Anderson and Mikhailovich who would be implementing these plans and adapting them to the actual situation.

"They're just scared." Anderson defended "None of them have seen what you've seen. We've all reviewed your reports, seen the data you've collected and some of the things coming out of your task force are just scary. But it's all just theory to us. You've been there in the trenches fighting them, Hell you even spoke to one and then blew the damned thing up, you know what they are capable of." "That why grounded me, took away my ship and stuck me behind a desk?" Jane asked with some heat to her voice. "You know that's not true. That shit in Bahak three hundred thousand Batarians died there. Anyone else would have been court marshaled and shot." Shepard knew this and knew she should have kept her temper in check better but damn it she wanted to be out there in the stars where she belonged.

"It's your knowledge of the Reapers that kept that from happening." "Sorry sir, I know that and your good word." Was Shepard's contrite reply.

"Yeah, I trust you Shepard and so does the comity. Else they would not have listened to any of your recommendations and design ideas."

"I'm just a soldier Anderson I'm not cut out for a desk job or head of a design group." Replied Shepard once again voicing her dismay about her current posting. "Listen we just need you to do whatever the hell it takes to stop the Reapers." This left Shepard wondering what was her old mentor was up to.

As the trio entered a set of sliding doors leading to a court rooms antechamber, they were met by a lieutenant-commander who was an aid to the comity. "There expecting you two, admiral." She said before leading them further to their destination. "Good luck in there commander." Said James signaling that this was as far as he went. The Commander figured as much one does not meet the defense comity in PT gear. Jane shook his hand and they exchanged a few words.

During this time Anderson met lieutenant-commander Ashley Willams "Anderson" She greeted the Admiral before noticing "Shepard". Jane turned at the sound of her name and recognized her old gunnery-chief from the Normandy SR-1. "Ashley?" She asked somewhat surprised to see her. "Lieutenant-commander," the Admiral began drawing her attention. "How did it go in there?" "I can never tell with them." Ashley never could read anyone worth a damn Shepard thought. "I'm just waiting for orders now."

"Admiral" reminded the aid who had been waiting unobtrusively off to the side. As Anderson and Shepard moved to follow the aid once again, Shepard could hear James and Ashley speaking "You know the commander?" asked the lieutenant of the lieutenant-commander. "I used to." was Ashleys reply reminding Shepard of the last time they had talked on Horizon, it had not gone well.

Shepard and Anderson entered the large courtroom that the comity was using. The aid had gone off to gather the Admirals of the comity. Shepard supposed it made sense to use one of the courtrooms it had all the communications gear they needed and could handle a lot of people and traffic.

"Admiral Anderson, Shepard" Greeted the head of the comity admiral Clarke. "What's the situation." asked Shepard jumping right in before there could be any speeches or her own doubts could fester. "We were hoping you could tell us." Clarke replied. A chief off to Shepard's right handed her a data pad, Shepard skimmed the information on it while Admiral McKee, spoke "The reports coming in are unlike anything we've seen. Whole colonies have gone dark, we've lost contact with everything beyond Arcturus." "Whatever this is, it's incomprehensibly powerful." finished admiral Clarke." Admiral Hackett has ordered the activation of all of our Anti-Reaper defenses including the minefields in Arcturus and Sol as well the Laser platforms and has begun supplying all ships with the anti-proton shells." Supplied admiral Whitt. Shepard looked up at the comity "I can only confirm what admiral Hackett already believes. The Reapers are here!" The room suddenly stilled at this everyone there had been clinging to the hope that it was something else, anything else.

"Will our preparations be enough?" asked admiral McKee in a small voice. "Depends how many there are and how effective our new systems will be in combat. In space we have a decent chance if they make planet fall however we will be hard pressed." Said Jane hoping that was true.

"Sirs, admiral Hackett is calling in, putting him on screen." came one of the techs.

The large screen showed static for a moment before the always grim face of the Chief of Naval Operations appeared. "Admirals, Commander. The Reapers have just come through the relay leading into Arcturus. They are taking heavy losses but are relentless. So far some five hundred Reapers of various sizes have come through including approximately one hundred Sovereign class Reapers in the vanguard." At this point the grim faced man chuckled "They ran right into the minefield. Those bomb pumped laser mines of yours did a number on them Shepard."

The bomb pumped x-ray laser mine was one of the ideas from Shepard's Ant-Reaper Task Force, it was in its simplest form just a 2 megaton nuclear bomb held in a magnetic bottle that would contain the detonation just long enough to focus the energy trough a laser tube. This made for an extremely powerful x-ray laser that had all the power of a 2 megaton nuclear weapon focused on an area the size of a dinner plate. When targeted at a Reaper the laser would be unaffected by the kinetic barrier because it was pure energy, then it would hit the hull and turn it into super heated plasma which in turn would expand rapidly, meaning inside of a microsecond, and either melt or simply blast apart more of the hull. While the laser itself would carry on into the interior of the Reaper wreaking havoc as it went. In theory at least but it seemed theory had proven correct.

"Every mine strike was a kill and every mine hit its target. That targeting VI cluster idea worked a treat." This was great news the VI cluster had been a worry. One hundred linked VI's picking targets together and prioritizing them working perfectly was a freaking miracle. Shepard breathed a sigh of relief at that. "Thank you sir" was al she could say. "Oh you haven't heard the best part yet," Shepard look at the admiral with interest, he looked oddly like a kid after getting that toy he wanted. "There was so much debris from the destroyed Reapers that there second wave almost completely self annihilated when they ran into them while trying to decelerate out of jump. Never seen a more beautiful sight in my life." Shepard blinked trying to imagine that sight and wishing she had been there. "This is were things start to get sticky." Hackett continued more gravely. "With the minefield gone the remains of the second and the complete third wave are up to the fleets here and our new laser defense platforms. We will be engaging them in the next half hour, but I can already see a lot of them heading for the relay to Sol you need to prepare. Activate your minefield, defense platforms and have the fleet unbox all the specials. I will inform you as soon as the situation here changes. Hackett out." The screen blanked and Hackett's face disappeared. Specials is the Alliance euphemism for all the things the Citadel conventions said they could not have, one of which was the bomb pumped lasers it was not the laser part that was illegal no it was the bomb part another were the anti-proton shells which were classified as anti-matter weapons.

Another NCO came up to Shepard and handed her another data pad this one containing telemetry from the mine strikes in Arcturus, the commander did a quick of the cuff analysis of the Reapers and what kind of damage the took and how. "Well commander, your thoughts?" prompted admiral McKee who was sounding much more upbeat and less defeated then before. "Admiral, to be frank it all comes down to numbers. I believe that if the Reapers do not send in heavy reinforcements immediately then we can hold Arcturus and Sol though some may make it to earth by simple blitz tactics. But that is just this space battle as I said my main concern is the ground battle and the shadow war we will have with the indoctrinated agents." "It's the indoctrinated we need to worry about they're the real threat now." Stated Anderson emphatically.

Shepard nodded at this, it was the one problem they had made no progress in. The space tech was relatively easy the concepts had existed for centuries but once element zero and the mass effect had been discovered these concepts and technologies had been abandoned. Sovereign had said it the relay network was a trap it locked them on a single technological path that the Reapers had chosen for the races of the galaxy and as any military officer will tell you doing what the enemy wants is a quick way to get dead. With that in mind and a secret group at her disposal Shepard went looking for these other technologies and oddly enough found most of them trough a classic science-fiction obsessed engineer in her group. He came to her with books in hand and showed her weapons that were not possible then but now they just might be.

"What progress have you made on the indoctrinated Shepard?" Asked admiral Whitt. "Very little sir. We simply do not have enough data, subjects or even examples of indoctrination to see how it works or how to combat it. The best we have so far is watching people for behavior that is out of character. But by then it might already be to late." Shepard hated admitting failure but there just was not enough to study. "We understand Shepard and we will have Alliance Intelligence begin monitoring for anything strange in there HumInt areas." Whitt was the planner charged with intelligence gathering operations.

"Sirs, I believe it is time to let the commander do what she does best and that is fight the Reapers anyway she can." Anderson was arguing on her behalf apparently to get her into the fight which was what she wanted but Jane had to wonder if she was missing something. Admiral McKee responded to Andersons statement in a way that truly floored Commander Jane Shepard "Yes yes, Anderson we know and Hackett has already approved her reinstatement to the command of the Normandy. Also we have vetted the crew that returned with her and most of them will be returning to her command." Shepard just goggled at this not really believing it when Clarke, who was desperately trying not to laugh at Shepard's truly surprised face, said to her "Come now Shepard this invasion has proven you right. That means the Council will be less likely to just dismiss you. That and your SPECTRE status of course." Anderson then spoke "The Council knows you they trusted you enough to make you a SPECTRE and you have been on top of the Reapers since you discovered them. You are the only choice to represent the Alliance in this." "I thought that was Udina's job." Sheppard's head was spinning she was getting her ship, the Normandy, back and getting into the fight but representing the Alliance as well was too much. Anderson explained they're thinking "Udina is a great Councilor in peace time, he is very good at all the political games, unlike me." "But we need a warrior to speak for us now and no matter what you say everyone knows you are an excellent orator and a natural leader." Finished admiral Clarke.

"So that's it Shepard. Report to the Normandy in dock eight, your orders and crew will be waiting for you there." The only thing Shepard could do was salute "Thank you sirs." about face and walk out to the anti-chamber.

In het anti-chamber she was met by Williams and Vega. "Lola is it true we have to report to the Normandy under your command?" Was the first thing out of Vega's mouth. "Yeah, well they gave me my command back but didn't say anything about you two." "Well our orders were just sent to us." Said Ashley holding up her omni-tool. "Then I guess we better get going." Jane said with finality and started moving with purpose towards the exit.

Once all three had arrived on the Normandy the voice of Joker came through the PA almost immediately "Shepard! Good to have you back." "Good to be back Joker." "The brass has ordered us to take off the moment you got onboard so hold on. And admiral Hackett is on the comm for you." That was a surprise and a worry the fleet battle in Arcturus could not have been going on long yet so either it was by some absurd miracle that the Alliance had won already or more likely it was a complete and total defeat. "Put him on Joker."

Hackett's face and prominent scar appeared on the screen with some static and drop outs but nothing to serious. "Shepard, I have already informed the fleets and the battle here has just started. We are taking losses but we are giving as good as we get." Shepard let out a breath she had not known she was holding. "The problem is almost half of the remaining Reapers are headed strait for Sol and I don't think the defenses there will hold them all." Shit this is bad if they make it to earth the death toll will be massive thought Shepard. "That's why I need you to go to Mars and pick up doctor T'Soni from the Mars Archives. She has been researching the Protheans and there war with the Reapers there and says she may have found something." Shepard blinked Liara was in system and hadn't ever called. "Also thought I should tell you those HVMs of yours are effective against Reapers, might take two to five hits to kill one of those things and only about half of them are actually on target but when they hit a Reaper it makes you remember why Sir Isaac Newton is so deadly in space. Telemetry and reports are on the way. Hackett out." Shepard suddenly realized she had not spoken a word during the entire transmission. Not like I could get a word in edge wise ran through her mind.

She was glad the Hyper Velocity Missiles were working though. The idea for them came from a brainstorm session about how to make main ship guns more powerful. Essentially the only real way was to make the projectile faster, but for that you needed a longer barrel that meant a bigger ship. Unless it could keep accelerating after it was fired and while projectiles fired from a gun could not, missiles with drives could and did. But to make a missile fast enough that it would carry enough kinetic energy to damage something like a Reaper it would have to be fired from a long way off and need to have more acceleration than any missile in the current inventory. The problem was solved by taking out the warhead of a disruptor torpedo and replacing it with a small eezo core not enough for faster than light but enough for ninety percent light speed inside of ten light seconds or about three million kilometers. The new weapon was a first strike weapon you fired it well outside normal ranges ten l/s or beyond and it would fly almost dead straight to your target accelerating the whole way there until it impacted the target. When it impacted the mass effect core, in the tip, that was lowering its mass to allow for its rapid speed would be the first thing destroyed, dropping the mass effect field and returning its full mass to the missile and then it was simple physics fourteen hundred kilos of missile at nine tenths the speed of light equals lots of power. Far more than the main gun of an Everest class dreadnought but this power would be blunted by kinetic barriers so the effect on a Reaper had still been up in the air. But apparently they worked and according to the incoming telemetry they worked reasonably well, no one hit kills but still. Damn Reapers are tough thought Jane.

Well no time for that she had a mission to complete. "Joker get us to the Mars Archives." "Mars? uh.. Okay commander." "Why are we going to Mars Lola?" asked Vega while walking up to join the commander by the armory. "We're picking up and old friend who Hackett says has information on the Reapers. So gear up and get ready." Shepard replied before checking her armor and making sure it would hold up to the environment on Mars. After having been spaced once she took this check far more seriously then anyone else. Dying by bullet or crushed by krogan was one thing but dying due to vacuum was truly horrifying and painful and not to be repeated. Half way through her checks her comm opened "Commander, CIC." "Go CIC." "Ma'am we are not receiving any response from the Mars Archives not even the automated beacons." Shepard ran through the options in her head for why that would be comm failure would explain not responding to hails but the beacons were meant to survive almost anything, for them not to be operating meant trouble. "CIC have the Reapers arrived at Mars already?" "No Ma'am the mine field around the Sol relay has just started going of as we are speaking ma'am." "Damn, thank you CIC we'll be ready down here." replied the commander before closing the channel. "Williams! Vega! We got trouble at the Archive get ready for combat."

**AN:** once again I hope you liked it and thank you for reading it. I don't know if I am going to continue it so if someone wants to adopt it just ask.  
>Also I know this story is a little science heavy but I read a lot of sci-fi and find concepts and ideas in one place that would work great in another and some just kinda stick. Just so you know I got the idea for the HVMs from the Odyssey One series which truly is sci-fi at its best and the bomb pumped lasers from the US DOD SDI program of the 1980s. I had several other ideas but have not found a way to get them into this story so who knows whats next.<p> 


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